fine-mapping

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability

The paper investigates the genetic contribution of organelles to age-related traits and finds that nuclear transcription factors have a greater influence on disease risk than other organelles.

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants

INFIMA identifies effector genes of GWAS variants by integrating multi-omics data from mice and applying it to diabetes-associated variants.

A UVB-responsive common variant at chr7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor gene (AHR)

This paper identifies rs117132860 as a functional variant at 7p21.1 that regulates AHR expression in response to UVB, contributing to melanoma risk and tanning ability.

The distribution of common-variant effect sizes

This paper estimates the distribution of common-variant effect sizes using GWAS summary statistics and finds that large sample sizes are needed to explain most heritability.

A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure

The paper presents a transcriptome for Botrychium lunaria, revealing population structure and improving phylogenetic resolution in early-branching ferns.

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

The paper identifies a 12 kb multi-allelic CNV associated with mastitis resistance in dairy cattle by linking it to increased GC expression and a cis-regulatory enhancer.

Fine-mapping of melanoma-associated genomic regions identifies novel causal SNPs in the MTAP/CDKN2A and CASP8 loci

The paper fine-maps melanoma-associated genomic regions to identify novel causal SNPs in the MTAP/CDKN2A and CASP8 loci using sequencing, variant filtering, and functional assays.

Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals

This study identifies 424 new loci associated with kidney function using GWAS data from over 1.2 million individuals and prioritizes 34 genes for further functional investigation.

The first insight into the genetic structure of the population of modern Serbia

This paper presents the first dataset of clinically relevant gene variants in the Serbian population, identifying unique genetic determinants and their potential health impacts.

Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses

The paper uses whole-exome imputation in UK Biobank to identify rare coding variant associations and fine-mapping results for 54 traits, finding 1,189 significant associations involving 675 novel variants.

Machine Learning based Genome-Wide Association Studies for Uncovering QTL Underlying Soybean Yield and its Components

This study uses machine learning algorithms in GWAS to identify QTL associated with soybean yield components, finding SVR outperforms conventional methods.

Significant East Asian affinity of Chinese Hui genomic structure suggesting their predominant cultural diffusion model in the genetic formation process

This study analyzes genomic data to determine the origin and genetic structure of Chinese Hui people, finding strong East Asian affinity and supporting a cultural diffusion model over demic diffusion.

Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

This study identifies causal variants, cells, genes, and drug targets for type 1 diabetes using large-scale genetic and functional genomic analyses.

Leveraging supervised learning for functionally-informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs

The paper uses supervised learning to fine-map cis-eQTLs, identifying 20,913 additional putative causal eQTLs and 310 candidate genes.

System genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose

The paper identifies Tti2 as a gene influencing both adult hippocampal neurogenesis and serum glucose levels using a rat genetic model.

A map of transcriptional heterogeneity and regulatory variation in human microglia

The paper profiles gene expression in human microglia from 141 patients, identifies population shifts in acute brain injury, maps eQTLs, and fine-maps Alzheimer's risk variants using hIPSC-derived macrophages.

Phenome-wide screening of GWAS data reveals the complex causal architecture of obesity

This study uses GWAS summary data to identify 110 traits with significant causal associations with obesity, revealing its broad impact on cardiovascular, anthropometric, and psychiatric conditions.

A New Functional F-Statistic for Gene-Based Inference Involving Multiple Phenotypes

The paper introduces an exact alternative to the Shen and Faraway F-statistic for gene-based multi-phenotype analysis, showing it performs well in small sample sizes and identifies novel associations in neurodegenerative disease data.

GWAS of Depression Phenotypes in the Million Veteran Program and Meta-analysis in More than 1.2 Million Participants Yields 178 Independent Risk Loci

This study identifies 178 independent risk loci for depression through a large meta-analysis across multiple cohorts, including fine-mapping and transcriptome-wide association findings.

Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants.

A coronary artery disease GWAS of 181,522 cases among 1,165,690 participants yields 241 associations (54 new); an eight-predictor consensus nominates 185 candidate causal genes, 94 with ≥3 predictors.

Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

The paper identifies cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation and links these to regulatory mechanisms of neuropsychiatric disorder risk variants.

Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk

This study combines large-scale GWAS and single-cell epigenomics to identify cell type-specific mechanisms of type 1 diabetes risk.

Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits and Diseases

The paper identifies an atlas of 3QTLs associated with alternative polyadenylation across 46 tissues, showing they explain 16.1% of trait-associated variants and contribute to disease independently of gene expression.

Joint analysis reveals shared autoimmune disease associations and identifies common mechanisms

The paper improves genetic mapping resolution in autoimmune diseases by identifying shared alleles across multiple conditions and reveals widespread shared mechanisms.

Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes

This study identifies glucocorticoid-responsive gene regulatory programs in pancreatic islets and links them to type 2 diabetes risk through chromatin and gene expression analysis.

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

MultiGWAS is a tool that performs GWAS for diploid and tetraploid organisms by integrating multiple software, improving reproducibility and model selection.

UTMOST, A Novel Single And Cross-Tissue TWAS (Transcriptome Wide Association Study), Reveals New ASD (Autism Spectrum Disorder) Associated Genes

UTMOST identifies new ASD-associated genes through single and cross-tissue TWAS, revealing associations in brain and gastrointestinal tissues.

The impact of non-additive genetic associations on age-related complex diseases.

This study applies an improved GWAS strategy to age-related diseases, identifying new genetic loci by using multiple reference panels, analyzing the X chromosome, and testing non-additive models.

Exploring Efficient Linear Mixed Models to Detect Quantitative Trait Locus-by-environment Interactions

This study compares linear mixed models to detect QTL and QTL-by-environment interactions in tomato phenotype data across cropping seasons.

Age-dependent genetic architecture underlines similar heritability of body size in sticklebacks

The paper shows that body size heritability remains constant in sticklebacks across ontogeny, but different genetic loci contribute to this heritability at different developmental stages.